Civilians affiliated with an enemy faction will call for help when they spot you nearby. Once they detect you, affiliated citizens stop what they’re doing and ask you to leave the area. They won’t take action against you, but they might draw armed enemies toward your location.
In most cases, you can simply ignore these citizens, while keeping around six or more feet away from them. They don’t usually cause too much trouble, and there are often route variations you can take to avoid confrontation with them. They are not enemies, and you should only react to them if they start calling out or phoning a faction.
With the former, simply melee strike them with a strangle, taser them, or use some nonlethal electrocution method. Or, simply move away from them to a hiding spot, wait for any alerted guards to return to their patrol, and continue.